The first part of your post is more of a personal opinion than a valid argument that really contributes nothing here.
Stellaris not being a balanced military strategy game is a claim, but it's claim that can be argued on non-subjective grounds. If it is true, it contributes significantly by pointing out that judging it on the grounds of being something it's not even trying to be is mis-aimed criticism.
If we were to judge Stellaris as a competitive multi-player military game, a large number of flaws would come up right away, from heavily-lopsided metas for existential competitiveness to large numbers of actively detrimental combos, to the fact that tactical positioning and control is nearly non-existent and the primary strategic decisions are in the economic, not deployment, background.
On the other hand, if we judge Stellaaris as single-player economic and/or roleplaying games, where war-making viability (and multiplayer) isn't the intended selling point the game is built around, then not all things being balanced around war is like noting that sand is not soft. It would be true, and largely irrelevant to core design decisions.
Would you stand by an argument that Stellaris fundamentally a multi-player military strategy game?
The second part is largely missing the point, while also leaving out huge chunks of what has been said so you can reach a fallacious conclusion. You don't need "tens of thousands" to terraform everything. You're on purpose leaving out both droids and migration pacts, as well as different difficulties being an option for the game, up to and including 25x crisis.
You do need tens of thousands to terraform more than a handful of planets, and for most of the early game the best migration pacts can get you is 80% habitability if you're RNG-lucky. For most of the early game- which is to say, when you're getting to a decisive position or not- you're not going to have +20% habitability from techs, and 10% is still a 10% gain even for right-biome species. This is why habitability gains are still useful even with migration pacts.
Similarly, Robots don't negate the benefits of boosting habitability because robots are never going to be your empire's only source of pop growth unless, well, you're a strictly robot empire. Which we aren't talking about. For organics who build robots, the organics are going to remain a key part of the economy throughout the game until/unless you synthetic-ascend them, and during that entire time
they would benefit from habitability even if you didn't.
That you talk about "most pop growth being natural" within the first century and describe it as early-ish is honestly quite telling. And no, the small number of pops won't make that big a difference. A single robot assembly plant will have a bigger impact. You're also simply assuming that you're somehow finishing the Yuht precursor in a time frame where you could still utilize it for the early game rush. That's not the case most of the time.
I'm not talking about any sort of rush. I'm talking about across the first century of a standard game, when planets are still in their growing phase and the economy is at it's most dynamic.
Even if we arbitrairly say that Yuht secrets are unlocked at year 30, and the player gets universal garden worlds/20% habitability-and-nothing-but-ideal-biomes types/synth ascension/whatever else makes habitability useless by year 60, a 30 year period of 5% organic population growth and 5% economic output from organic pops is going to be considerably significant. This is the point in most games where a 5% will matter
most- whether in pre-empting mid-game rivals, or getting investments that will acrue with time.
And that's if we limit it to just 30 years. Depending on your builds, it could go much further.